2020(S08) Lecture:week 8

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Week 8 Tuesday

This week you will spend nearly all of our lecture and studio time specifying these aspects of your project:

  • a system overview
  • a device list
  • a timing diagram
  • a parts list

It's unlikely you'll be "done" with any of them by the time the week ends, especially since you may need to revise what seemed like completed aspects of your project as you learn more about what's available and how things work. Design/revise/design/revise/design/revise....

Challenge: System Overview: Flip Books or Phase Wheel

  • Here's a warm up challenge to show what is meant by a system overview
    • Option 1: Working independently, you should take 10 minutes to sketch a process into a flip book (materials to be provided). The process you choose to illustrate is up to you. It can be a plant growing, a house of cards being built, or a happy message appearing letter by letter on a computer screen. What you choose is limited only by the number of pages in your book, your ability to draw, and the limited amount of time we've given you to complete this challenge. 10 minutes only!
    • Option 2: The moon and the sun move through the earth's sky in a predictable pattern. Working independently, you can assemble a lunar phase wheel that illustrates this pattern. The phase wheel (materials to be provided) is a device that was developed by Dr. Mary Urquhart at the University of Texas at Dallas. It represents our view of the sky, the different appearances the moon can take in our sky, and the movement of each lunar phase relative to the sun. In 10 minutes you should be able to assemble the lunar phase wheel and use it to answer the following questions in your project design notebook:
      • At sunrise, where is the sun relative to the horizon?
      • At sunrise, where is a full moon relative to the horizon?
      • Moving the sun from sunrise to sunset, is the full moon visible during the day?
      • What kinds of moon(s) are visible for the greatest number of daylight hours?
    • Before we move on to the next part of today's class we'll hear from some of the flip-book drawers and some of the lunar phase wheelers to learn what worked well and what didn't about each device in terms of providing an overview of the system to be illustrated.
  • Next you and your project team will generate a system overview for the Melbourne 2007 iGEM "coliform" project
    • The Melbourne team wanted to build a 3D, floating mass of bacteria that adhered to one another when the cells detected both blue and red light. In other words: at the intersection of an incoming red light beam and blue light beam, a solution of bacteria would clump and remain suspended in its growth media.
coliformers from Melbourne's iGEM 2007 team
coliformers from Melbourne's iGEM 2007 team
    • As a class we'll watch the first 5 minutes of the Melbourne team's iGEM presentation
    • Next your project team should work out a system overview for the coliform project. You can either get an unused flip book (or use the back of one from the warmup exercise), turn the lunar phase wheel over, or come up with some other mechanism of illustrating how the Melbourne team's system would work. You should not spend more than 10 minutes on this activity. When you are done, give the overview to one of the team mentors to hand in or explain to Drew and Natalie. You and your team can get right to work on the last thing planned for today's lecture.
  • Finally, take the rest of today's lecture time to illustrate or specify the system overview of your team's project. You do not need to make either flip books or phase wheels unless you find these useful ways to brainstorm and define the outstanding issues. Ideally the system overview you generate today will be shown in your Tech Spec Review, that is happening one week from tomorrow (eek!).

Before tomorrow's studio time

If there are outstanding issues related to the system overview for your project be sure everyone on your team knows how you'll solve the issue(s) and make a plan to come to studio tomorrow with materials for finishing the system overview and getting good work done on the device list and the timing diagram.

Week 8 Studio

Part 1: Wrap-up System Overview

You will have time to polish up any leftover work on this aspect of your project once we have introduced device lists and timing diagrams.

Part 2: Generate Device list and Timing Diagram

Consider again the coliform project from the Melbourne 2007 iGEM team. The team listed six devices they needed to realize their idea:

  1. a red light sensor
  2. a blue light sensor
  3. an AND gate to trigger a cellular behavior when both lights are present
  4. a GFP reporter to monitor easily/quantifiably the AND gate's function
  5. expression of adhesive proteins under the control of the AND gate
  6. a gas vesicle expression cassette to produce neutrally buoyant bacteria

Working with your project team at the white boards, list the six devices on a y-axis and time on an x-axis and then indicate the timing for operation of each device, including the persistence of each device's signal through time. You can keep a running list of any uncertainties. After 15 minutes of work, we'll have each team report back to the group, and then you can spend the rest of today's studio time working on a device list and timing diagram for your own project.

In case this is helpful, here is a timing diagram for the IAP 2004 Polkadork's Ecoli-brator project
timing diagram for the Polkadork's Ecolibrator project

Week 8 Thursday

Challenge: Time is $$

==Mapping these ideas to your project==
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